My wife had struggles very similar to yours. She had herself tested for a super broad range of allergies and intolerances (this wasn't cheap) and found that her histamine levels were 20x the upper bound of "normal". This was in a time when eating a single chocolate chip cookie could knock her out for days.

She then did an elimination diet much like yours (but without the keto - she just cut out anything that either is high in histamine or encourages histamine production in the body). She's a different person now. Her gut mostly recovered in the sense that the same cookie would now make her feel bad for a few hours and sometimes not even that. It's great.

Just in case it interests someone, she maintains a food blog particular for histamine intolerant people at https://histaminefriendlykitchen.com/